Signatures of Selection Among de novo Assembled Transcriptomes of Four White Pine Species

Conifers are evolutionarily ancient group of trees that form the dominant vegetation throughout the northern boreal forests of high latitude regions of North America, Europe, and Asia. They possess exceptional longevity and play an integral economic and ecological role across much of the world. Here we investigate de novo assembled transcriptomes of four white pine species: western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana). All are five-needle white pines classified as members of the subgenus Strobus. Among them Pinus monticola, Pinus flexilis, and Pinus albicaulis are high elevation species and will be largely affected by climate change. Annotation of the four white pine needle leaf tissue transcriptomes sequenced using Illumina next generation platform revealed a core set of 2025 gene families shared across the four white pines among which 408 showed signatures of selection. Of these 408, 39 are estimated to be under positive selection (average dN/dS > 1), 9 are under neutral selection (average dN/dS < 1 and average dN/dS > 0.95), and the remaining 360 are under purifying selection (average dN/dS <0.95). Among the positively selected genes FBK-Skip6, E3 Ubiquitin Protein Ligase and UTP7 will be highlighted. A comparative study examining the gene space among the four species including candidate genes involved in drought tolerance, disease and pest resistance and phenology is underway. Adaptive evolution and patterns of selection among the four white pines will advance our understanding of this ancient non-model plant group. This study complements Sugar Pine Genome project gene models by providing full-length transcripts.